We had previously identified 11 isolates of Streptococcus pyogenes that were resistant to fluoroquinolones and we identified point mutations in the quinolone resistance determining regions (QRDR) of the parC and gyrA genes. More recently, we amplified and sequenced the QRDRs of the parE and gyrB genes and found no point mutations. The M type of each isolated was determined by an outside laboratory. We evaluated Rep-PCR to study strain relatedness of our isolates and found that the S. pyogenes RepPCR patterns are the same for each M-type. Therefore this method of molecular typing is not useful to determine strain relatedness among isolates of the same M type. We found that Pulsed Field Gel Electrophoresis provided much more discriminatory power and we were able to demonstrate strain differences among isolates with the same M type.